suppressPackageStartupMessages(library(circlize))
suppressPackageStartupMessages(library(cowplot))
suppressPackageStartupMessages(library(ggbeeswarm))
suppressPackageStartupMessages(library(ggplot2))
suppressPackageStartupMessages(library(kableExtra))
suppressPackageStartupMessages(library(knitr))
suppressPackageStartupMessages(library(reshape2))
suppressPackageStartupMessages(library(grid))
source('~/scripts/ocean_mag_hgt/scripts/cooccur_phylo_hgt/explore_correlation_code.R')

Overall filter-split summary

Pairwise Spearman correlations

allsamples_blast_pairwise_in <- read_in_pairwise("/mfs/gdouglas/projects/ocean_mags/networks/allsamples/blast/partial_corr_out_median/", approaches, suffix = ".pairwise.tsv")
allsamples_ranger_pairwise_in <- read_in_pairwise("/mfs/gdouglas/projects/ocean_mags/networks/allsamples/rangerdtl/partial_corr_out_median/", approaches, suffix = ".pairwise.tsv")
allsamples_clusterbased_pairwise_in <- read_in_pairwise("/mfs/gdouglas/projects/ocean_mags/networks/allsamples/clusterbased/partial_corr_out_median/", approaches, suffix = ".pairwise.tsv")

freeliv_blast_pairwise_in <- read_in_pairwise("/mfs/gdouglas/projects/ocean_mags/networks/filtersplit/blast/partial_corr_out_median/", approaches, suffix = "_freeliv.pairwise.tsv")
freeliv_ranger_pairwise_in <- read_in_pairwise("/mfs/gdouglas/projects/ocean_mags/networks/filtersplit/rangerdtl/partial_corr_out_median/", approaches, suffix = "_freeliv.pairwise.tsv")
# freeliv_clusterbased_pairwise_in <- read_in_pairwise("/mfs/gdouglas/projects/ocean_mags/networks/filtersplit/clusterbased/partial_corr_out_median/", approaches, suffix = "_freeliv.pairwise.tsv")

lessfiltered_blast_pairwise_in <- read_in_pairwise("/mfs/gdouglas/projects/ocean_mags/networks/filtersplit/blast/partial_corr_out_median/", approaches, suffix = "_lessfiltered.pairwise.tsv")
lessfiltered_ranger_pairwise_in <- read_in_pairwise("/mfs/gdouglas/projects/ocean_mags/networks/filtersplit/rangerdtl/partial_corr_out_median/", approaches, suffix = "_lessfiltered.pairwise.tsv")
# lessfiltered_clusterbased_pairwise_in <- read_in_pairwise("/mfs/gdouglas/projects/ocean_mags/networks/filtersplit/clusterbased/partial_corr_out_median/", approaches, suffix = "_lessfiltered.pairwise.tsv")

BLAST all samples results

RANGER all samples results

Cluster-based all samples results

BLAST free-living results

RANGER-DTL free-living results

BLAST less-filtered results

RANGER-DTL less-filtered results

Partial Spearman correlations

blast_allsamples <- read_partial_corr_output("/mfs/gdouglas/projects/ocean_mags/networks/allsamples/blast/partial_corr_out_median/", "both_gene_count", approaches)
ranger_allsamples <- read_partial_corr_output("/mfs/gdouglas/projects/ocean_mags/networks/allsamples/rangerdtl/partial_corr_out_median/", "ranger_hgt_tallies", approaches)

blast_freeliv <- read_partial_corr_output("/mfs/gdouglas/projects/ocean_mags/networks/filtersplit/blast/partial_corr_out_median/", "both_gene_count", paste(approaches, "freeliv", sep = '_'))
ranger_freeliv <- read_partial_corr_output("/mfs/gdouglas/projects/ocean_mags/networks/filtersplit/rangerdtl/partial_corr_out_median/", "ranger_hgt_tallies", paste(approaches, "freeliv", sep = '_'))

blast_lessfiltered <- read_partial_corr_output("/mfs/gdouglas/projects/ocean_mags/networks/filtersplit/blast/partial_corr_out_median/", "both_gene_count", paste(approaches, "lessfiltered", sep = '_'))
ranger_lessfiltered <- read_partial_corr_output("/mfs/gdouglas/projects/ocean_mags/networks/filtersplit/rangerdtl/partial_corr_out_median/", "ranger_hgt_tallies", paste(approaches, "lessfiltered", sep = '_'))

clusterbased_allsamples <- read_partial_corr_output("/mfs/gdouglas/projects/ocean_mags/networks/allsamples/clusterbased/partial_corr_out_median/", "both_gene_count", approaches)
# clusterbased_freeliv <- read_partial_corr_output("/mfs/gdouglas/projects/ocean_mags/networks/filtersplit/clusterbased/partial_corr_out_median/", "both_gene_count", paste(approaches, "freeliv", sep = '_'))
# clusterbased_lessfiltered <- read_partial_corr_output("/mfs/gdouglas/projects/ocean_mags/networks/filtersplit/clusterbased/partial_corr_out_median/", "both_gene_count", paste(approaches, "lessfiltered", sep = '_'))

BLAST all samples

RANGER all samples

Cluster-based all samples

BLAST free-living

RANGER free-living

BLAST less-filtered

RANGER less-filtered

Session info

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sessionInfo()
## R version 4.4.0 (2024-04-24)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.4 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0 
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
## 
## locale:
##  [1] LC_CTYPE=en_CA.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_CA.UTF-8        LC_COLLATE=en_CA.UTF-8    
##  [5] LC_MONETARY=en_CA.UTF-8    LC_MESSAGES=en_CA.UTF-8   
##  [7] LC_PAPER=en_CA.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C       
## 
## time zone: America/Toronto
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] grid      stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
## [1] reshape2_1.4.4   knitr_1.48       kableExtra_1.4.0 ggbeeswarm_0.7.2
## [5] ggplot2_3.5.1    cowplot_1.1.3    circlize_0.4.16 
## 
## loaded via a namespace (and not attached):
##  [1] gtable_0.3.5          beeswarm_0.4.0        shape_1.4.6.1        
##  [4] rjson_0.2.23          xfun_0.48             bslib_0.8.0          
##  [7] GlobalOptions_0.1.2   vctrs_0.6.5           tools_4.4.0          
## [10] generics_0.1.3        stats4_4.4.0          parallel_4.4.0       
## [13] tibble_3.2.1          fansi_1.0.6           highr_0.11           
## [16] cluster_2.1.2         pkgconfig_2.0.3       RColorBrewer_1.1-3   
## [19] S4Vectors_0.42.1      lifecycle_1.0.4       farver_2.1.2         
## [22] compiler_4.4.0        stringr_1.5.1         munsell_0.5.1        
## [25] codetools_0.2-18      ComplexHeatmap_2.20.0 clue_0.3-65          
## [28] vipor_0.4.7           htmltools_0.5.8.1     sass_0.4.9           
## [31] yaml_2.3.10           pillar_1.9.0          crayon_1.5.3         
## [34] jquerylib_0.1.4       cachem_1.1.0          iterators_1.0.14     
## [37] foreach_1.5.2         tidyselect_1.2.1      digest_0.6.37        
## [40] stringi_1.8.4         dplyr_1.1.4           labeling_0.4.3       
## [43] fastmap_1.2.0         colorspace_2.1-1      cli_3.6.3            
## [46] magrittr_2.0.3        utf8_1.2.4            withr_3.0.1          
## [49] scales_1.3.0          rmarkdown_2.28        matrixStats_1.4.1    
## [52] png_0.1-8             GetoptLong_1.0.5      evaluate_1.0.0       
## [55] IRanges_2.38.1        doParallel_1.0.17     viridisLite_0.4.2    
## [58] rlang_1.1.4           Rcpp_1.0.13           glue_1.8.0           
## [61] xml2_1.3.6            BiocGenerics_0.50.0   svglite_2.1.3        
## [64] rstudioapi_0.16.0     jsonlite_1.8.9        R6_2.5.1             
## [67] plyr_1.8.9            systemfonts_1.1.0